Cyclin D1 promoter

Maximilian Haeussler via methods%40net.bio.net (by maximilianh from gmail.com)
Thu May 15 11:25:34 EST 2008


I think this question should be sent to a bioinformatics-mailing-list like
the BBB (http://www.bioinformatics.org/pipermail/bio_bulletin_board/)

Short answer: Depends on what do you want to find.  I guess you want to
compare binding sites. I assume that you don't want to align them, (if you
did, then simply type dna alignment into google)

Links of all of the tools that I am citing here can be found at the Wiki for
tools on Transcriptional Regulation on openwetware.com:
http://openwetware.org/wiki/Tregwiki:Main_Page

I dont' think that there is a very usable tool for this task. Comparison of
un-alignable cis-regulatory sequences is very strange topic and there is not
good usable tool yet. You should have an idea of the type of transcription
factor that is binding there. But you can try Matinspector from genomatix in
any case, it's very easy to use.

There is FamilyRelations from Titus Brown which can compare short words in a
set of sequences and is creating a graphical representation of them. There
are some recent publications that have been benchmarked on the even-skipped
enhancer in drosophila and they can often find the orthologous enhancer in
other un-alignable species but they are usually not available as websites
and you better know a bit about programming to use them.

cheers,
Max



2008/5/15 Debashish Das <debashish.das from ki.se>:

> Hi
>
> I am interested in looking for the promoter of Cyclin D1 and compare that
> across species. I
> would be very grateful if anyone here could provide me with any website
> where not only can
> I find the promoter of the gene of my interest as well as would be able to
> compare it across
> the species.
>
> thanking you all in advance!
>
>
>
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>



-- 
Maximilian Haeussler,
tel: +33 6 12 82 76 16


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